Exegesis is a procedure to refine the gene predictions that are produced for complex genomes, e.g. those of humans and mice. It uses the program Genewise, sequences determined by experiment, experimental maps of gene segment libraries and a new browser that allows the user to rapidly inspect and compare multiple gene maps to regions of genomic sequences. The procedure should be of general use. Here, we use the procedure to find members of the immunoglobulin superfamily in the human and mouse genomes. To do this, Exegesis was used to process the original gene predictions from the automated Ensembl annotation pipeline. Exegesis produced (i) many more complete genes and new transcripts and (ii) a mapping of the immunoglobulin and T cell receptor gene libraries to the genome, which are largely absent in the Ensembl set.